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Parkourtest #208

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Parkourtest #208

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c06b512
Main (#204)
WardDeb Aug 16, 2024
6c2f902
update install docu
thomasmanke Dec 1, 2024
a803bc3
fix parkour organism as list
thomasmanke Dec 1, 2024
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ Clone this repository, create the environment and pip install

> git clone [email protected]:maxplanck-ie/dissectBCL.git
> cd dissectBCL
> conda create -f env.yml --name dissectBCL
> conda env create -f env.yml --name dissectBCL
> conda activate dissectBCL
> pip install ./

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4 changes: 2 additions & 2 deletions src/dissectBCL/fakeNews.py
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Expand Up @@ -443,7 +443,7 @@ def gatherFinalMetrics(outLane, flowcell):
# hence the try / except.
# 'mouse (GRCm39)' -> 'mouse'
parkourOrg = str( # To string since NA is a float
ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0]
ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0][0]
).split(' ')[0]
try:
screenDF = pd.read_csv(
Expand Down Expand Up @@ -478,4 +478,4 @@ def gatherFinalMetrics(outLane, flowcell):
'transferTime': flowcell.transferTime,
'exitStats': flowcell.exitStats,
'P5RC':ssDic['P5RC']
}
}
4 changes: 2 additions & 2 deletions src/dissectBCL/misc.py
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Expand Up @@ -510,7 +510,7 @@ def multiQC_yaml(flowcell, project, laneFolder):
))
# Organisms
orgs = ', '.join(list(
ssdf["Organism"].fillna('None').unique()
ssdf["Organism"].str[0].fillna('None').unique()
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))
# Resequencing runs are screwed up (e.g. don't contain the samples)
# switch total requested to NA
Expand Down Expand Up @@ -663,4 +663,4 @@ def matchOptdupsReqs(optDups, ssdf):
int(got)
]
)
return (sorted(_optDups, key=lambda x: x[1]))
return (sorted(_optDups, key=lambda x: x[1]))
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